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<h1 class="epydoc">Source Code for <a href="dadi-module.html">Package dadi</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt>  <tt class="py-line"><tt class="py-docstring">For examples of dadi's usage, see the examples directory in the source</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt>  <tt class="py-line"><tt class="py-docstring">distribution.</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt>  <tt class="py-line"><tt class="py-docstring">Documentation of all methods can be found in doc/api/index.html of the source</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt>  <tt class="py-line"><tt class="py-docstring">distribution.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">logging</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt>  <tt class="py-line"><tt class="py-name">logging</tt><tt class="py-op">.</tt><tt class="py-name">basicConfig</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt>  <tt class="py-line"> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Module dadi.Demographics1D=dadi.Demographics1D-module.html"><a title="dadi.Demographics1D" class="py-name" href="#" onclick="return doclink('link-0', 'Demographics1D', 'link-0');">Demographics1D</a></tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Module dadi.Demographics2D=dadi.Demographics2D-module.html"><a title="dadi.Demographics2D" class="py-name" href="#" onclick="return doclink('link-1', 'Demographics2D', 'link-1');">Demographics2D</a></tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Module dadi.Inference=dadi.Inference-module.html"><a title="dadi.Inference" class="py-name" href="#" onclick="return doclink('link-2', 'Inference', 'link-2');">Inference</a></tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Module dadi.Integration=dadi.Integration-module.html"><a title="dadi.Integration" class="py-name" href="#" onclick="return doclink('link-3', 'Integration', 'link-3');">Integration</a></tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-4" class="py-name" targets="Module dadi.Misc=dadi.Misc-module.html"><a title="dadi.Misc" class="py-name" href="#" onclick="return doclink('link-4', 'Misc', 'link-4');">Misc</a></tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-5" class="py-name" targets="Module dadi.Numerics=dadi.Numerics-module.html"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-5', 'Numerics', 'link-5');">Numerics</a></tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-6" class="py-name" targets="Module dadi.PhiManip=dadi.PhiManip-module.html"><a title="dadi.PhiManip" class="py-name" href="#" onclick="return doclink('link-6', 'PhiManip', 'link-6');">PhiManip</a></tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt>  <tt class="py-line"><tt class="py-comment"># Protect import of Plotting in case matplotlib not installed.</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt>  <tt class="py-line"><tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt id="link-7" class="py-name" targets="Module dadi.Plotting=dadi.Plotting-module.html"><a title="dadi.Plotting" class="py-name" href="#" onclick="return doclink('link-7', 'Plotting', 'link-7');">Plotting</a></tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt>  <tt class="py-line"><tt class="py-keyword">except</tt> <tt class="py-name">ImportError</tt><tt class="py-op">:</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt>  <tt class="py-line">    <tt class="py-keyword">pass</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt>  <tt class="py-line"> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt>  <tt class="py-line"><tt class="py-comment"># We do it this way so it's easier to reload.</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-8" class="py-name" targets="Module dadi.Spectrum_mod=dadi.Spectrum_mod-module.html"><a title="dadi.Spectrum_mod" class="py-name" href="#" onclick="return doclink('link-8', 'Spectrum_mod', 'link-8');">Spectrum_mod</a></tt>  </tt>
<a name="L26"></a><tt class="py-lineno">26</tt>  <tt class="py-line"><tt id="link-9" class="py-name" targets="Variable dadi.Demographics1D.Spectrum=dadi.Spectrum_mod.Spectrum-class.html,Variable dadi.Demographics2D.Spectrum=dadi.Spectrum_mod.Spectrum-class.html,Class dadi.Spectrum_mod.Spectrum=dadi.Spectrum_mod.Spectrum-class.html"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-9', 'Spectrum', 'link-9');">Spectrum</a></tt> <tt class="py-op">=</tt> <tt id="link-10" class="py-name"><a title="dadi.Spectrum_mod" class="py-name" href="#" onclick="return doclink('link-10', 'Spectrum_mod', 'link-8');">Spectrum_mod</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-11', 'Spectrum', 'link-9');">Spectrum</a></tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt>  <tt class="py-line"> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt>  <tt class="py-line"><tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt>  <tt class="py-line">    <tt class="py-comment"># This is to try and ensure we have a nice __SVNVERSION__ attribute, so</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt>  <tt class="py-line">    <tt class="py-comment"># when we get bug reports, we know what version they were using. The</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt>  <tt class="py-line">    <tt class="py-comment"># svnversion file is created by setup.py.</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt>  <tt class="py-line">    <tt id="link-12" class="py-name" targets="Variable dadi._directory=dadi-module.html#_directory"><a title="dadi._directory" class="py-name" href="#" onclick="return doclink('link-12', '_directory', 'link-12');">_directory</a></tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">dirname</tt><tt class="py-op">(</tt><tt id="link-13" class="py-name"><a title="dadi.Integration" class="py-name" href="#" onclick="return doclink('link-13', 'Integration', 'link-3');">Integration</a></tt><tt class="py-op">.</tt><tt class="py-name">__file__</tt><tt class="py-op">)</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt>  <tt class="py-line">    <tt id="link-14" class="py-name" targets="Variable dadi._svn_file=dadi-module.html#_svn_file"><a title="dadi._svn_file" class="py-name" href="#" onclick="return doclink('link-14', '_svn_file', 'link-14');">_svn_file</a></tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt id="link-15" class="py-name"><a title="dadi._directory" class="py-name" href="#" onclick="return doclink('link-15', '_directory', 'link-12');">_directory</a></tt><tt class="py-op">,</tt> <tt class="py-string">'svnversion'</tt><tt class="py-op">)</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt>  <tt class="py-line">    <tt id="link-16" class="py-name" targets="Variable dadi.__SVNVERSION__=dadi-module.html#__SVNVERSION__"><a title="dadi.__SVNVERSION__" class="py-name" href="#" onclick="return doclink('link-16', '__SVNVERSION__', 'link-16');">__SVNVERSION__</a></tt> <tt class="py-op">=</tt> <tt class="py-name">file</tt><tt class="py-op">(</tt><tt id="link-17" class="py-name"><a title="dadi._svn_file" class="py-name" href="#" onclick="return doclink('link-17', '_svn_file', 'link-14');">_svn_file</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">read</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt>  <tt class="py-line"><tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt>  <tt class="py-line">    <tt id="link-18" class="py-name"><a title="dadi.__SVNVERSION__" class="py-name" href="#" onclick="return doclink('link-18', '__SVNVERSION__', 'link-16');">__SVNVERSION__</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'Unknown'</tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt>  <tt class="py-line"> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt>  <tt class="py-line"><tt class="py-comment"># When doing arithmetic with Spectrum objects (which are masked arrays), we</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt>  <tt class="py-line"><tt class="py-comment"># often have masked values which generate annoying arithmetic warnings. Here</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt>  <tt class="py-line"><tt class="py-comment"># we tell numpy to ignore such warnings. This puts greater onus on the user to</tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt>  <tt class="py-line"><tt class="py-comment"># check results, but for our use case I think it's the better default.</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">numpy</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt>  <tt class="py-line"><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">seterr</tt><tt class="py-op">(</tt><tt class="py-name">all</tt><tt class="py-op">=</tt><tt class="py-string">'ignore'</tt><tt class="py-op">)</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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